Calculate euclidean or along the network distance between points located in one basin

Calculate euclidean or along-the-network distance (in meters) between points located in one basin. To calculate the distance along the network, point coordinates need to be snapped to the stream network using the function snap_to_network() or snap_to_subc_segment().

Usage

get_distance(
  data,
  lon,
  lat,
  id,
  stream_layer = NULL,
  distance = "both",
  n_cores = 1,
  quiet = TRUE
)

Arguments

data: a data.frame or data.table that contains the columns regarding the longitude / latitude coordinates in WGS84.
lon: character. The name of the column with the longitude coordinates.
lat: character. The name of the column with the latitude coordinates.
id: character. The name of a column containing unique IDs for each row of "data" (e.g., occurrence or site IDs). The unique IDs need to be numeric and less than 10 characters long.
stream_layer: character. Full path of the stream network .gpkg file. Needs to be defined to calculate the distance along the network. (In the case of Hydrography90m, the relevant files have the format "order_vect_segment_h??v??.gpkg")
distance: character. One of "euclidean", "network", or "both". If "euclidean", the euclidean distances between all pairs of points are calculated. If "network", the shortest path along the network between all pairs of points is calculated. (see "Details" for more information). If method is set to "both", both distance measures are calculated. Distances are given in meters. Default is "both".
n_cores: numeric. Number of cores used for parallelisation. Default is 1.
quiet: logical. If FALSE, the standard output will be printed. Default is TRUE.

Value

If distance='euclidean', a distance matrix, in meters, of the euclidean distances between all the pairs of points (object of class data.frame) is returned. If distance='network', a data.frame with three columns: from_id, to_id, dist is returned. The 'dist' column includes the distance, in meters, of the shortest path along the network from the point "from_id" to the point "to_id". If distance='both', a list containing both objects is returned.

Details

To calculate the euclidean distance between all pairs of points the function uses the v.distance command of GRASS GIS, which has been set up to produce a square matrix of distances. The calculation of distances along the stream network has been implemented with the command v.net.allpairs of GRASS GIS. The along-the-network distance calculation is done for all pairs of points located within the same basin. If the points are located in different basins, the function get_distance_parallel() should be used.

References

https://grass.osgeo.org/grass82/manuals/v.net.allpairs.html https://grass.osgeo.org/grass82/manuals/v.distance.html

Author

Afroditi Grigoropoulou, Marlene Schürz, Jaime Garcia Marquez

Examples

# Download test data into the temporary R folder
# or define a different directory
my_directory <- tempdir()
download_test_data(my_directory)

# Load occurrence data
species_occurrence <- read.table(paste0(my_directory,
                            "/hydrography90m_test_data/spdata_1264942.txt"),
                              header = TRUE)

basin_rast <- paste0(my_directory,
                     "/hydrography90m_test_data/basin_1264942.tif")

# Define full path to the sub-catchment raster layer
subc_rast <- paste0(my_directory,
                    "/hydrography90m_test_data/subcatchment_1264942.tif")

# Define full path to the vector file of the stream network
stream_vect <- paste0(my_directory,
                      "/hydrography90m_test_data/order_vect_59.gpkg")

# Automatically extract the basin and sub-catchment IDs and
# snap the data points to the stream segment
snapped_coordinates <- snap_to_subc_segment(data = species_occurrence,
                                            lon = "longitude",
                                            lat = "latitude",
                                            id = "occurrence_id",
                                            basin_layer = basin_rast,
                                            subc_layer = subc_rast,
                                            stream_layer = stream_vect,
                                            n_cores = 2)
# Show head of output table
head(snapped_coordinates)

# Get the euclidean distance and the distance along the network between all
# pairs of points
distance_table <- get_distance(data = snapped_coordinates,
                               lon = "lon_snap",
                               lat = "lat_snap",
                               id = "occurrence_id",
                               stream_layer = stream_vect,
                               distance = "network")
# Show table
distance_table